I installed a new Synology NAS with two folder shares with encryption enabled. The Synology is configured to check for updates, but not install them. This is so we can control that this is performed when there is no backup activity going on. After installing the updates the NAS is automatically rebooted.
After the reboot when I went to make sure I could still access the file shares on the device, I discovered they appeared to be gone. In a panic, I checked the disk volumes within the Synology Web UI and saw they still had quite a bit of used disk space, so the data was still there.
As it turns out, the shared folders need to be mounted after a reboot. Select each shared folder and under the encryption dropdown will be an option to mount. This will bring up a prompt for the encryption key password which you must provide. After mounting the folders, I could access the file shares again over CIFS.